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Published 20 hours ago • verified publisher icon Bibliome

Command-line interface install fails on MacOS 10

Open mdorf opened this issue 5 years ago • 2 comments 

▲ dev/alvis_test/alvisnlp ▶ bash --version
GNU bash, version 3.2.57(1)-release (x86_64-apple-darwin18)
Copyright (C) 2007 Free Software Foundation, Inc.

▲ dev/alvis_test/alvisnlp ▶ brew info coreutils                                                                                                                                                                                                                  master :: 27d :: ⬡
coreutils: stable 8.31 (bottled), HEAD

I am not sure about the version of locate.

Trying to run the installer script yields the following output:

Running via Bash:

bash-3.2$ ./install.sh /Users/mdorf/dev/alvis_test/alvisnlp/
readlink: illegal option -- m
usage: readlink [-n] [file ...]
Install directory:
Default parameter values file: share/default-param-values.xml
Default options file: share/default-options.txt
mkdir: : No such file or directory
cp: illegal option -- u
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
       cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory
cp: illegal option -- u
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
       cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory
cp: illegal option -- u
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
       cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory
./install.sh: line 450: /bin/alvisnlp: Operation not permitted
chmod: /bin/alvisnlp: No such file or directory

Running via ZSH:

▲ dev/alvis_test/alvisnlp ▶ sudo ./install.sh -i /Users/mdorf/dev/alvis_test/alvisnlp                                                                                                                                                     master :: 27d :: ⬡
Password:
Interactive mode for third-party tools

Defaults for EnjuParser
locate: illegal option -- -
usage: locate [-0Scims] [-l limit] [-d database] pattern ...

default database: `/var/db/locate.database' or $LOCATE_PATH
./install.sh: line 129: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]

Defaults for CCGParser and CCGPosTagger
locate: illegal option -- -
usage: locate [-0Scims] [-l limit] [-d database] pattern ...

default database: `/var/db/locate.database' or $LOCATE_PATH
./install.sh: line 149: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]
./install.sh: line 160: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]

Defaults for GeniaTagger
locate: illegal option -- -
usage: locate [-0Scims] [-l limit] [-d database] pattern ...

default database: `/var/db/locate.database' or $LOCATE_PATH
./install.sh: line 173: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]

Defaults for StanfordNER

WARNING: The locate database (/var/db/locate.database) does not exist.
To create the database, run the following command:

  sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.locate.plist

Please be aware that the database can take some time to generate; once
the database has been created, this message will no longer appear.

./install.sh: line 184: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]

Defaults for TreeTagger
locate: illegal option -- -
usage: locate [-0Scims] [-l limit] [-d database] pattern ...

default database: `/var/db/locate.database' or $LOCATE_PATH
./install.sh: line 195: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]

Defaults for YateaExtractor and TomapTrain
locate: illegal option -- -
usage: locate [-0Scims] [-l limit] [-d database] pattern ...

default database: `/var/db/locate.database' or $LOCATE_PATH
./install.sh: line 213: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]

Defaults for TEESTrain and TEESClassify
locate: illegal option -- -
usage: locate [-0Scims] [-l limit] [-d database] pattern ...

default database: `/var/db/locate.database' or $LOCATE_PATH
./install.sh: line 237: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]

Defaults for Chemspot
locate: illegal option -- -
usage: locate [-0Scims] [-l limit] [-d database] pattern ...

default database: `/var/db/locate.database' or $LOCATE_PATH
./install.sh: line 255: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]

Defaults for Word2Vec, ContesTrain and ContesPredict
locate: illegal option -- -
usage: locate [-0Scims] [-l limit] [-d database] pattern ...

default database: `/var/db/locate.database' or $LOCATE_PATH
./install.sh: line 266: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]

Defaults for Species
locate: illegal option -- -
usage: locate [-0Scims] [-l limit] [-d database] pattern ...

default database: `/var/db/locate.database' or $LOCATE_PATH
./install.sh: line 290: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]

Defaults for Ab3P
locate: illegal option -- -
usage: locate [-0Scims] [-l limit] [-d database] pattern ...

default database: `/var/db/locate.database' or $LOCATE_PATH
./install.sh: line 301: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]

Defaults for WapitiTrain WapitiLabel
locate: illegal option -- -
usage: locate [-0Scims] [-l limit] [-d database] pattern ...

default database: `/var/db/locate.database' or $LOCATE_PATH
./install.sh: line 312: read: -i: invalid option
read: usage: read [-ers] [-u fd] [-t timeout] [-p prompt] [-a array] [-n nchars] [-d delim] [name ...]

Done at last!

readlink: illegal option -- m
usage: readlink [-n] [file ...]
Install directory:
Default parameter values file: .default-param-values.xml
Default options file: share/default-options.txt
mkdir: : No such file or directory
cp: illegal option -- u
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
       cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory
cp: illegal option -- u
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
       cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory
cp: illegal option -- u
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
       cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory
./install.sh: line 450: /bin/alvisnlp: Operation not permitted
chmod: /bin/alvisnlp: No such file or directory

▲ dev/alvis_test/alvisnlp ▶

mdorf avatar Oct 10 '19 22:10 mdorf

Hi, the ./install.sh script uses options only available in the GNU version of Core Utils. In MacOS X, these tools only accept POSIX options.

If GNU Core Utils is installed, I can easily target the binaries instead of the default ones.

I am currently fixing install.sh so it checks the OS and make sure that the GNU version is used.

rbossy avatar Oct 17 '19 12:10 rbossy

I've managed to run the install script on a MacOS:

brew install coreutils
PATH="/usr/local/opt/coreutils/libexec/gnubin:$PATH"
./install.sh DIR

The first line installs the GNU version of coreutils. The second replaces the MacOS version with the GNU version in the path.

We should include a test in the install script.

rbossy avatar Mar 29 '22 17:03 rbossy